AMN
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That's quite helpful, thanks! I am still concerned about cases like the one I mentioned, but it is good to know that overall this gave you the best results.
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Hi Genevieve, We are still looking into the differences. However a preliminary look at the first few lines shows some differences already. The 42nd and 43rd line of the bam: spark-enabled: $ samto...
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Sure, I took a single bam and produced two sorted bams with SortSam, one queryname-sorted and the other coordinate-sorted. I ran MarkDuplicates on each one the same way except for the `--ASSUME_SOR...
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Hi Genevieve, Thanks for your reply. I tried MarkDuplicatesSpark and the results seem to match ReadsPipelineSpark rather than our implementation of MarkDuplicates. sample totalreads_MarkDuplicate...
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Hi Genevieve, Thank you for your reply. I have generated a small table comparing the results of each (one using GATK 4.1.9.0 MarkDuplicates, the other using GATK 4.1.9.0 ReadsPipelineSpark). here'...
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I am finding that MarkDuplicates and this tool ReadsPipelineSpark mark a different number of reads as duplicate (flag > 1024). Same version of gatk (4.1.0.0). Why is this the case? any configuratio...